CellProfiler
{{Short description|Image processing software}}
{{Infobox Software
| name = CellProfiler
| logo = CellProfiler logo 2017.png
| developer = Anne E. Carpenter, Thouis Jones, Lee Kamentsky, Beth Cimini, Allen Goodman, Claire McQuin, Madison Swain-Bowden, David Stirling, Nodar Gogoberidze, and others (Broad Institute)
| latest_release_version = 4.2.1
| latest_release_date = {{Start date and age|2021|07|22}}
| operating_system = Any (Python-based)
| genre = Image processing & Image analysis
| license = BSD 3-clause
| website = {{URL|www.cellprofiler.org}}
}}
CellProfiler{{cite journal |vauthors=Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, Golland P, Sabatini DM |title=CellProfiler: image analysis software for identifying and quantifying cell phenotypes |journal=Genome Biology |volume=7|issue=10 |pages=R100 |year=2006|pmid=17076895 |doi= 10.1186/gb-2006-7-10-r100 |pmc=1794559 |doi-access=free }}{{cite journal |vauthors=Kamentsky L, Jones TR, Fraser A, Bray MA, Logan DJ, Madden KL, Ljosa V, Rueden C, Eliceiri KW, Carpenter AE |title=Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software |journal=Bioinformatics |volume=27 |issue=8 |pages=1179–80 |date=April 2011|pmid=21349861 |doi= 10.1093/bioinformatics/btr095|pmc=3072555}} is free, open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. Advanced algorithms for image analysis are available as individual modules that can be placed in sequential order together to form a pipeline; the pipeline is then used to identify and measure
biological objects and features in images, particularly those obtained through fluorescence microscopy.
Distributions are available for Microsoft Windows, macOS, and Linux. The source code for CellProfiler is freely available.{{cite web |url=https://github.com/CellProfiler/CellProfiler/wiki |title=CellProfiler wiki|author= |date= December 2016 |website=GitHub}} CellProfiler is developed by the Broad Institute's Imaging Platform.{{cite web |url=http://www.broadinstitute.org/science/platforms/imaging/imaging-platform |title=Imaging Platform|author= |date= 2018 |website=Broad Institute}}
Features
CellProfiler can read and analyze most common microscopy image formats.{{Cite web|url=http://www.openmicroscopy.org/site/support/bio-formats5.2/users/cellprofiler/|title=CellProfiler — Bio-Formats 5.2.1 documentation|website=www.openmicroscopy.org|access-date=2016-08-29}}{{Dead link|date=November 2019 |bot=InternetArchiveBot |fix-attempted=yes }} Biologists typically use CellProfiler to identify objects of interest (e.g. cells, colonies, C. elegans worms) and then measure their properties of interest.{{Cite journal|last1=Lamprecht|first1=Michael R.|last2=Sabatini|first2=David M.|last3=Carpenter|first3=Anne E.|date=2007-01-01|title=CellProfiler: free, versatile software for automated biological image analysis|journal=BioTechniques|volume=42|issue=1|pages=71–75|issn=0736-6205|pmid=17269487|doi=10.2144/000112257|doi-access=free}} Specialized modules for illumination correction may be applied as pre-processing step to remove distortions due to uneven lighting.{{Cite journal|last1=Singh|first1=S.|last2=Bray|first2=M.-A.|last3=Jones|first3=T. R.|last4=Carpenter|first4=A. E.|date=2014-12-01|title=Pipeline for illumination correction of images for high-throughput microscopy|journal=Journal of Microscopy|volume=256|issue=3|pages=231–236|doi=10.1111/jmi.12178|issn=1365-2818|pmc=4359755|pmid=25228240}} Object identification (segmentation) is performed through machine learning or image thresholding, recognition and division of clumped objects, and removal or merging of objects on the basis of size or shape.{{Cite web|url=http://d1zymp9ayga15t.cloudfront.net/CPmanual/IdentifyPrimaryObjects.html|title=IdentifyPrimaryObjects|website=d1zymp9ayga15t.cloudfront.net|access-date=2016-08-29}} Each of these steps are customizable by the user for their unique image assay.
A wide variety of measurements can be generated for each identified cell or subcellular compartment, including morphology, intensity, and texture among others. These measurements are accessible by using built-in viewing and plotting data tools, exporting in a comma-delimited spreadsheet format,{{Cite web|url=http://d1zymp9ayga15t.cloudfront.net/CPmanual/ExportToSpreadsheet.html|title=ExportToSpreadsheet|website=d1zymp9ayga15t.cloudfront.net|access-date=2016-08-29}} or importing into a MySQL or SQLite database.{{Cite web|url=http://d1zymp9ayga15t.cloudfront.net/CPmanual/ExportToDatabase.html|title=ExportToDatabase|website=d1zymp9ayga15t.cloudfront.net|access-date=2016-08-29}}
CellProfiler interfaces with the high-performance scientific libraries NumPy and SciPy for many mathematical operations, the Open Microscopy Environment{{cite web |url=http://openmicroscopy.org |title=Open Microscopy Environment |author= |access-date=2018-05-07}} Consortium’s Bio-Formats library for reading more than 100 image file formats, ImageJ for use of plugins and macros, and ilastik for pixel-based classification.{{Cite web|url=https://github.com/CellProfiler/CellProfiler/wiki/How-to-use-Pixel-Classification-in-CellProfiler|title=CellProfiler/CellProfiler|website=GitHub|access-date=2016-08-29}} While designed and optimized for large numbers of two-dimensional images (the most common high-content screening image format), CellProfiler supports analysis of small-scale experiments and time-lapse movies.{{Cite journal|last1=Bray|first1=Mark-Anthony|last2=Carpenter|first2=Anne E.|date=2015-01-01|title=CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data|journal=BMC Bioinformatics|volume=16|pages=368|doi=10.1186/s12859-015-0759-x|issn=1471-2105|pmc=4634901|pmid=26537300 |doi-access=free }}
History
CellProfiler was released in December 2005 by scientists from the Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology.{{Cite journal|title=What Is the Key Best Practice for Collaborating with a Computational Biologist?|journal=Cell Systems|volume=3|issue=1|pages=7–11|doi=10.1016/j.cels.2016.07.006|pmid=27467242|year=2016|doi-access=free}} It is currently developed and maintained by the Cimini Lab at the Imaging Platform of the Broad Institute.{{cite web |url=https://cimini-lab.broadinstitute.org/ |title=Cimini Lab |access-date=2022-08-10}}
Originally developed in MATLAB, it was re-written in Python and released as CellProfiler 2.0 in 2010. Version 3.0, supporting volumetric analysis of 3D image stacks and optional deep learning modules, was released in October 2017.{{cite web |url=https://blog.cellprofiler.org/2017/10/16/cellprofiler-3-0-release-faster-better-and-3d/ |title=CellProfiler 3.0 release: faster, better, and 3D |author=Carpenter, AE |date=2017-10-16 |website= CellProfiler Blog}} CellProfiler 4.0 was released in September 2020 and focused on speed, usability, and utility improvements with most notable example of migration to Python 3.{{Cite web|title=CellProfiler 4.0 Release: Improvements in speed, utility, and usability|url=https://carpenterlab.broadinstitute.org/blog/cellprofiler-40-release-improvements-speed-utility-and-usability|access-date=2020-10-16|website=carpenterlab.broadinstitute.org|language=en}}
Community
Because CellProfiler is a free, open-source project, anyone can develop their own image processing algorithms as a new module for CellProfiler and contribute it to the project.{{Cite web|url=https://github.com/CellProfiler/CellProfiler/wiki/Module-structure-and-data-storage-retrieval|title=CellProfiler/CellProfiler|website=GitHub|access-date=2016-08-29}} The CellProfiler website contains a forum for discussion where new users can have their questions answered, usually by the creators of the project.{{Cite web|url=http://forum.cellprofiler.org/|title=CellProfiler|website=forum.cellprofiler.org|access-date=2016-08-29}}
References
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External links
{{Portal|Free and open-source software}}
- {{Official website|cellprofiler.org}}
{{Image_Processing_Software}}
{{DEFAULTSORT:Cellprofiler}}